On 12/18/2017 05:39 AM, Eleanor Dodson wrote:
I showed you pdbset ..
Find the centre of mass for your assembly.
Move it where you will
Thanks. What James was suggesting was somewhat different (if I understood
correctly): move EVERY ATOM to 1,1,1.
like:
awk -v FIELDWIDTHS="30 24 26" \
'$1~/ATOM|HETATM/ && $2=" 1.000 1.000 1.000" {print $1 $2 $3}' \
3AEF.pdb
Then his origins program will find the symop/origin transform that moves the
protein closest to that point. But come to think of it, moving COM to that
point would probably have the same effect. Need to think about a lop-sided
2-domain protein, where the symop is going to switch the orientation of
large/small domains, and the large domain is negative of the com putting it
outside the cell. but the com will be offset into the large domain, so probably
still ok.
ORIGINS does assume like atoms have the same chain/resno in the different
structures, which is not the case for 3AEF and friends, but they are close
enough that it gives the right answer anyway.
pdbset xyzin mow.pdb
end
Find CoM 0.7 1.3 -0.2
Hmm - a little thought - centre at 1 -1 0 say
pdbset yzin now.pdb xyzout changed.pdb
symgen x , y-2, z
end
New CoM 0.7 -0.7 -0.2
Eleanor
On 18 December 2017 at 00:19, Edward A. Berry <[email protected]
<mailto:[email protected]>> wrote:
Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1?
or 0.1,0.1,0.1 if I still want it near the origin but biased toward the inside
of the positive-going cell?
eab
On 12/14/2017 07:23 PM, James Holton wrote:
What I usually do for this is make a copy of the PDB file and change all the atom x-y-z positions to
"1.000". Then I use something like reforigin or my "origins.com <http://origins.com>"
script to shift the original coordinates via allowed symmetry operations, origin shifts, or perhaps indexing
ambiguities until it is as close as possible to the "reference", which is at 1,1,1. I use 1,1,1 instead
of 0,0,0 because there are generally at least two symmetry-equivalent places that are equidistant from the origin.
Declaring the reference to be a bit off-center breaks that ambiguity, and also biases the result toward having
all-positive x,y,z values.
In case it is interesting, my script is here:
http://bl831.als.lbl.gov/~jamesh/scripts/origins.com
<http://bl831.als.lbl.gov/~jamesh/scripts/origins.com>
You need to have the CCP4 suite set up for it to work. Run it with no
arguments to get instructions.
-James Holton
MAD Scientist
On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:
Hello,
If someone could point this out would be very helpful... Wasnt
there a simple script somewhere that would transfer coordinates close to origin
- if they for some reason are not? Just cant find anything right away. Sure i
have done this before...
Thanks,
Tommi
